Browsing by Subject "PHYLOGENY"

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  • Turzhanova, Ainur; Khapilina, Oxana; Tumenbayeva, A; Shevtsov, Vladislav; Raiser, Olesya; Kalendar, Ruslan (2020)
    The genus Alternaria is a widely distributed major plant pathogen that can act as a saprophyte in plant debris. Fungi of this genus frequently infect cereal crops and cause such diseases as black point and wheat leaf blight, which decrease the yield and quality of cereal products. A total of 25 Alternaria sp. isolates were collected from germ grains of various wheat cultivars from different geographic regions in Kazakhstan. We investigated the genetic relationships of the main Alternaria species related to black point disease of wheat in Kazakhstan, using the inter-primer binding site (iPBS) DNA profiling technique. We used 25 retrotransposon-based iPBS primers to identify the differences among and within Alternaria species populations, and analyzed the variation using clustering (UPGMA) and statistical approaches (AMOVA). Isolates of Alternaria species clustered into two main genetic groups, with species of A.alternata and A.tennuissima forming one cluster, and isolates of A. infectoria forming another. The genetic diversity found using retrotransposon profiles was strongly correlated with geographic data. Overall, the iPBS fingerprinting technique is highly informative and useful for the evaluation of genetic diversity and relationships of Alternaria species.
  • Asfaw, Beimnet; Aserse, Aregu Amsalu; Asefa, Fassil; Yli-Halla, Markku; Lindstrom, Kristina (2020)
    In total 196 bacterial isolates were obtained from root nodules of lentil (Lens culinaris) and faba bean (Vicia faba) grown on soil samples collected from 10 different sites in central and southern parts of Ethiopia. All isolates were identified as members of the genus Rhizobium by using recA gene sequence analysis. In the recA phylogenetic tree 195 rhizobial strains were classified into nine genospecies. The phylogeny of symbiotic genes nodC and nifH revealed five and six distinct groups respectively, largely dominated by symbiovar viciae. A multivariate analysis showed that environmental variables of the sampling sites considered in this study had more effect on the distribution and composition of the genospecies than the host legumes of the strains. Twenty representative strains, selected based on their isolation site, host plant and nodC group, were able to nodulate all lentil, faba bean, field pea (Pisum abyssinicum) and grass pea (Lathyrus sativus) plants in a greenhouse test in axenic conditions. The majority of the rhizobial strains were effective nitrogen-fixing symbionts for all tested legumes, indicating their potential to serve as broad host-range inoculants in agriculture. The present work suggests the presence of taxonomically and symbiotically diverse rhizobial species for legumes in the Viciae tribe in Ethiopia.
  • Biersma, E. M.; Jackson, J. A.; Hyvonen, J.; Koskinen, S.; Linse, K.; Griffiths, H.; Convey, P. (2017)
    A bipolar disjunction is an extreme, yet common, biogeographic pattern in non-vascular plants, yet its underlyingmechanisms (vicariance or long-distance dispersal), origin and timing remain poorly understood. Here, combining a large-scale population dataset and multiple dating analyses, we examine the biogeography of four bipolar Polytrichales mosses, common to the Holarctic (temperate and polar Northern Hemisphere regions) and the Antarctic region (Antarctic, sub-Antarctic, southern South America) and other Southern Hemisphere (SH) regions. Our data reveal contrasting patterns, for three species were of Holarctic origin, with subsequent dispersal to the SH, while one, currently a particularly common species in the Holarctic (Polytrichum juniperinum), diversified in the Antarctic region and from here colonized both the Holarctic and other SH regions. Our findings suggest long-distance dispersal as the driver of bipolar disjunctions. We find such inter-hemispheric dispersals are rare, occurring on multi-million-year timescales. High-altitude tropical populations did not act as trans-equatorial 'steppingstones', but rather were derived from later dispersal events. All arrivals to the Antarctic region occurred well before the Last Glacial Maximum and previous glaciations, suggesting that, despite the harsh climate during these past glacial maxima, plants have had a much longer presence in this southern region than previously thought.
  • Hosseinzadeh, Mahboubeh Sadat; Farhadi Qomi, Masood; Naimi, Babak; Roedder, Dennis; Kazemi, Seyed Mandi (2018)
    Species distribution models estimate the relationship between species occurrences and environmental and spatial characteristics. Herein, we used maximum entropy distribution modelling (MaxEnt) for predicting the potential distribution of the Plateau Snake Skink Ophiomorus nuchalis on the Iranian Plateau, using a small number of occurrence records (i.e. 10) and environmental variables derived from remote sensing. The MaxEnt model had a high success rate according to test AUC scores (0.912). A remotely sensed enhanced vegetation index (39.1%), and precipitation of the driest month (15.4%) were the most important environmental variables that explained the geographical distribution of O. nuchalis. Our results are congruent with previous studies suggesting that suitable habitat of O. nuchalis is limited to the central Iranian Plateau, although mountain ranges in western and eastern Iran might be environmentally suitable but not accessible.
  • Liu, Zhigao; Korpelainen, Helena (2018)
    Currently, there is a lack of genetic markers capable of effectively detecting polymorphisms in Clematis. Therefore, we developed new markers to investigate inter- and intraspecific diversity in Clematis. Based on the complete chloroplast genome of Clematis terniflora, simple sequence repeats were explored and primer pairs were designed for all ten adequate repeat regions (cpSSRs), which were tested in 43 individuals of 11 Clematis species. In addition, the nuclear ITS region was sequenced in 11 Clematis species. Seven cpSSR loci were found to be polymorphic in the genus and serve as markers that can distinguish different species and be used in different genetic analyses, including cultivar identification to assist the breeding of new ornamental cultivars.
  • Shishido, Tania Keiko; Wahlsten, Matti; Laine, Pia; Rikkinen, Jouko; Lundell, Taina; Auvinen, Petri (2021)
    Lichens have been widely used in traditional medicine, especially by indigenous communities worldwide. However, their slow growth and difficulties in the isolation of lichen symbionts and associated microbes have hindered the pharmaceutical utilisation of lichen-produced compounds. Advances in high-throughput sequencing techniques now permit detailed investigations of the complex microbial communities formed by fungi, green algae, cyanobacteria, and other bacteria within the lichen thalli. Here, we used amplicon sequencing, shotgun metagenomics, and in silico metabolomics together with compound extractions to study reindeer lichens collected from Southern Finland. Our aim was to evaluate the potential of Cladonia species as sources of novel natural products. We compared the predicted biosynthetic pathways of lichen compounds from isolated genome-sequenced lichen fungi and our environmental samples. Potential biosynthetic genes could then be further used to produce secondary metabolites in more tractable hosts. Furthermore, we detected multiple compounds by metabolite analyses, which revealed connections between the identified biosynthetic gene clusters and their products. Taken together, our results contribute to metagenomic data studies from complex lichen-symbiotic communities and provide valuable new information for use in further biochemical and pharmacological studies.
  • Santana, Antonita; Silva, Sofia Marques; Batista, Romina; Sampaio, Iracilda; Aleixo, Alexandre (2021)
    The true diversity and interspecific limits in the Neotropical endemic avian genusDendrocolaptes(Furnariidae) remain a highly controversial subject, with previous genus-wide assessments, based mostly on morphological characters, producing poorly resolved phylogenies. The lack of well-resolved, robust, and taxonomically densely sampled phylogenies forDendrocolaptesprevents reliable inferences on the genus' actual species diversity and evolutionary history. Here, we analyzed 2,741 base pairs of mitochondrial and nuclear genes from 43 specimens belonging to all species and the majority of subspecies described forDendrocolaptesto evaluate species limits and reconstruct its diversification through time. Our phylogenies recovered a monophyleticDendrocolaptes, with two main highly supported internal clades corresponding to theD. certhiaandD. picumnusspecies complexes. Also, our analyses supported the monophyly of mostDendrocolaptesspecies recognized today, exceptD. picumnus, which was consistently recovered as paraphyletic with respect toD. hoffmannsi. A coalescent-based test supported a total of 15 different lineages inDendrocolaptesand indicated that the number of currently accepted species within the genus may be greatly underestimated. Particularly relevant, when combined with previous analyses based on plumage characters, comparative high levels of genetic differentiation and coalescent analyses support the recognition ofD. picumnus transfasciatusas a full species that is already under threat. Ancestral area reconstructions suggest that diversification inDendrocolapteswas centered in lowland Amazonia, with several independent dispersal events leading to differentiation into different adjacent dry and high elevation forest types throughout the Neotropics, mainly during the Middle and Late Pleistocene.
  • Twort, Victoria G.; Minet, Joël; Wheat, Christopher W.; Wahlberg, Niklas (2021)
    Museomics is a valuable approach that utilizes the diverse biobanks that are natural history museums. The ability to sequence genomes from old specimens has expanded not only the variety of interesting taxa available to study but also the scope of questions that can be investigated in order to further knowledge about biodiversity. Here, we present whole genome sequencing results from the enigmatic genus Whalleyana (comprising two species - occurring in drier biomes of Madagascar - previously placed in a monotypic superfamily, Whalleyanoidea), as well as from certain species of the families Callidulidae and Hyblaeidae (Calliduloidea and Hyblaeoidea, respectively). Library preparation was carried out on four museum specimens and one existing DNA extract and sequenced with Illumina short reads. De novo assembly resulted in highly fragmented genomes with the N50 ranging from 317 to 2078 bp. Mining of a manually curated gene set of 331 genes from these draft genomes had an overall gene recovery rate of 64-90%. Phylogenetic analysis places Whalleyana as sister to Callidulidae and Hyblaea as sister to Pyraloidea. Since the former sister-group relationship turns out to be also supported by ten morphological synapomorphies, we propose to formally assign the Whalleyanidae to the superfamily Calliduloidea. These results highlight the usefulness of not only museum specimens but also existing DNA extracts, for whole genome sequencing and gene mining for phylogenomic studies.
  • Spirin, Viacheslav; Malysheva, Vera; Miettinen, Otto; Vlasak, Josef; Mendes Alvarenga, Renato Lucio; Gibertoni, Tatiana Baptista; Ryvarden, Leif; Larsson, Karl-Henrik (2019)
    The taxonomy of Protomerulius and Heterochaetella is revised based on DNA data and morphological evidence, and their type species, P. brasiliensis and H. dubia, are proved to be congeneric. As a consequence, H. dubia and related species, of which four are described as new, are placed in Protomerulius. Heterochaete microspora is also combined in Protomerulius, and the genus concept is redefined to encompass effused species with smooth or spiny hymenophore and monomitic hyphal structure. Psilochaete multifora, gen. and spec. nov. is a distant relative of Protomerulius spp. found in Norway. Heterochaetella cystidiophora is re-collected in Brazil and placed in the synonyms of Heterochaete sanctae-catharinae. This species does not belong to the Protomerulius-Heterochaetella lineage, and it is transferred to Metulochaete, gen. nov.
  • Koblmüller, Stephan; Zangl, Lukas; Börger, Christine; Daill, Daniel; Vanhove, Maarten P. M.; Sturmbauer, Christian; Sefc, Kristina M. (2019)
    In the absence of dispersal barriers, species with great dispersal ability are expected to show little, if at all, phylogeographic structure. The East African Great Lakes and their diverse fish faunas provide opportunities to test this hypothesis in pelagic fishes, which are presumed to be highly mobile and unrestricted in their movement by physical barriers. Here, we address the link between panmixis and pelagic habitat use by comparing the phylogeographic structure among four deepwater cichlid species of the tribe Bathybatini from Lake Tanganyika. We show that the mitochondrial genealogies (based on the most variable part or the control region) of the four species are very shallow (0.8–4% intraspecific divergence across entire distribution ranges) and that all species experienced recent population growth. A lack of phylogeographic structure in the two eupelagic species, Bathybates fasciatus and B. leo, was consistent with expectations and with findings in other pelagic cichlid species. Contrary to expectations, a clear phylogeographic structure was detected in the two benthopelagic species, B. graueri and Hemibates stenosoma. Differences in genetic diversity between eupelagic and benthopelagic species may be due to differences in their dispersal propensity, mediated by their respective predatory niches, rather than precipitated by external barriers to dispersal.
  • Woronik, Alyssa; Stefanescu, Constanti; Käkelä, Reijo; Wheat, Christopher W.; Lehmann, Philipp (2018)
    Across a wide range of taxa, individuals within populations exhibit alternative life history strategies (ALHS) where their phenotypes dramatically differ due to divergent investments in growth, reproduction and survivorship, with the resulting trade-offs directly impacting Darwinian fitness. Though the maintenance of ALHS within populations is fairly well understood, little is known regarding the physiological mechanisms that underlie ALHS and how environmental conditions can affect the evolution and expression of these phenotypes. One such ALHS, known as Alba, exists within females of many species in the butterfly genus Colias. Previous works in New World species not only found that female morphs differ in their wing color due to a reallocation of resources away from the synthesis of wing pigments to other areas of development, but also that temperature played an important role in these trade-offs. Here we build on previous work conducted in New World species by measuring life history traits and conducting lipidomics on individuals reared at hot and cold temperatures in the Old World species Colias croceus. Results suggest that the fitness of Alba and orange morphs likely varies with rearing temperature, where Alba females have higher fitness in cold conditions and orange in warm. Additionally shared traits between Old and New World species suggest the Alba mechanism is likely conserved across the genus. Finally, in the cold treatment we observe an intermediate yellow morph that may have decreased fitness due to slower larval development. This cost may manifest as disruptive selection in the field, thereby favoring the maintenance of the two discrete morphs. Taken together these results add insights into the evolution of, and the selection on, the Alba ALHS.
  • Heikkilä, Maria; Brown, John W.; Baixeras, Joaquin; Mey, Wolfram; Kozlov, Mikhail V. (2018)
    We re-evaluate eleven fossils that have previously been assigned to the family Tortricidae, describe one additional fossil, and assess whether observable morphological features warrant confident assignment of these specimens to this family. We provide an overview of the age and origin of the fossils and comment on their contribution towards understanding the phylogeny of the Lepidoptera. Our results show that only one specimen, Antiquatortia histuroides Brown & Baixeras gen. and sp. nov., shows a character considered synapomorphic for the family. Six other fossils (Electresia zalesskii Kusnezov, 1941; Tortricidrosis inclusa Skalski, 1973; Tortricites skalskii Kozlov, 1988; Tortricibaltia diakonoffi Skalski, 1992; Polyvena horatis Poinar and Brown, 1993 and a trace fossil purported to be larval feeding damage of Retinia resinella (Linnaeus, 1758)) exhibit a combination of homoplastic characters typical of tortricid moths or characteristic feeding damage. An unnamed species doubtfully assigned to Olethreutinae by Skalski (1992), Spatalistiforma submerga Skalski, 1992, Tortricites florissantanus (Cockerell, 1907), Tortricites destructus (Cockerell, 1916) and Tortricites sadilenkoi Kozlov, 1988 do not show enough character evidence to be convincingly placed in Tortricidae. Therefore, we transfer the three latter species from the collective group Tortricites Kozlov, 1988, defined as an assemblage of fossil leafrollers that cannot be placed with certainty in known genera, to Paleolepidopterites Kozlov, new collective group, defined as a group of fossil lepidopterans whose assignment to a certain family is currently impossible.
  • Rikkinen, Jouko; Beimforde, Christina; Seyfullah, Leyla; Perrichot, Vincent; Schmidt, Kerstin; Schmidt, Alexander (2016)
    A novel species of ascomycetes is described from resin of Araucaria humboldtensis on Mont Humboldt in New Caledonia. The fungus is placed in the new genus Resinogalea Rikkinen & A.R. Schmidt, with the species name R. humboldtensis Rikkinen & A.R. Schmidt. It has only been found growing on semi-hardened resin flows on branches of its endemic and endangered conifer host. The morphology and anatomy of the new fungus are compared with those of ecologically similar taxa, including Bruceomyces castoris. The new family Bruceomycetaceae Rikkinen & A.R. Schmidt is described to accommodate Resinogalea and Bruceomyces.
  • Malysheva, Vera; Spirin, Viacheslav; Miettinen, Otto; Motato-Vasquez, Viviana; Hernawati,; Seelan, Jaya Seelan Sathiya; Larsson, Karl-Henrik (2018)
    Three species currently addressed to Protohydnum (Auriculariales) are studied with morphological and DNA methods. The genus Protohydnum is retained for the type species only, P. cartilagineum, recently re-collected in Brazil. The European species, P. piceicola, is not congeneric with P. cartilagineum and, therefore, placed in its own genus, Hyalodon, gen. nov. Another Hyalodon species, H. antui, is described from East Asia. The third member of Protohydnum sensu lato, P. sclerodontium from South-East Asia, is transferred to Elmerina.
  • Schmidt, Alexander R.; Regalado, Ledis; Weststrand, Stina; Korall, Petra; Sadowski, Eva-Maria; Schneider, Harald; Jansen, Eva; Bechteler, Julia; Krings, Michael; Müller, Patrick; Wang, Bo; Wang, Xin; Rikkinen, Jouko; Seyfullah, Leyla J. (2020)
  • Geraerts, Mare; Muterezi Bukinga, Fidel; Vanhove, Maarten P. M.; Pariselle, Antoine; Chocha Manda, Auguste; Vreven, Emmanuel; Huyse, Tine; Artois, Tom (2020)
    Background Monogenea van Beneden, 1858 is a group of parasitic flatworms, commonly found infecting bony fish. Several genera, such as Cichlidogyrus Paperna, 1960, are reported to include potential pathogenic species that can negatively impact aquaculture fish stocks. They can switch from introduced to native fish and vice versa. In Africa (and all over the world), fish species belonging to Cichlidae are often kept in aquaculture and represent a major source of food. Thus, research on the biodiversity and occurrence of monogenean species on these fish is of importance for aquaculture and conservation. The present study is a survey of the diversity of species of Cichlidogyrus in the south of the Democratic Republic of the Congo (DRC) on three cichlid species: Orthochromis sp. 'Lomami', Serranochromis cf. macrocephalus, and Tilapia sparrmanii Smith, 1840. Methods Specimens of Cichlidogyrus were isolated from the gills and mounted on glass slides with Hoyer's medium. The genital and haptoral hard parts were measured and drawn using interference contrast. Results In total, six species of Cichlidogyrus were found, all new to science: C. bulbophallus n. sp. and C. pseudozambezensis n. sp. on S. cf. macrocephalus, C. flagellum n. sp. and C. lobus n. sp. on T. sparrmanii, C. ranula n. sp. on S. cf. macrocephalus and Orthochromis sp. 'Lomami', and C. maeander n. sp. found on Orthochromis sp. 'Lomami' and T. sparrmanii. The first four species are considered to be strict specialists, C. ranula n. sp. an intermediate generalist and C. maeander n. sp. a generalist. These parasite species show morphological similarities to species found in the Lower Guinea and Zambezi ichthyofaunal provinces, which might be explained by past river capture events between river systems of the Congo Province and both these regions. Conclusions Serranochromis cf. macrocephalus and Orthochromis sp. 'Lomami' can harbour respectively three and two species of Cichlidogyrus, all described in this study. Tilapia sparrmanii can harbour seven species, of which three are described in the present study. These results highlight the species diversity of this parasite genus in the Congo Basin.
  • Gafforov, Yusufjon; Ordynets, Alexander; Langer, Ewald; Yarasheva, Manzura; de Mello Gugliotta, Adriana; Schigel, Dmitry; Pecoraro, Lorenzo; Zhou, Yu; Cai, Lei; Zhou, Li-Wei (2020)
    Uzbekistan, located in Central Asia, harbors high diversity of woody plants. Diversity of wood-inhabiting fungi in the country, however, remained poorly known. This study summarizes the wood-inhabiting basidiomycte fungi (poroid and corticoid fungi plus similar taxa such as Merismodes, Phellodon, and Sarcodon) (Agaricomycetes, Basidiomycota) that have been found in Uzbekistan from 1950 to 2020. This work is based on 790 fungal occurrence records: 185 from recently collected specimens, 101 from herbarium specimens made by earlier collectors, and 504 from literature-based records. All data were deposited as a species occurrence record dataset in the Global Biodiversity Information Facility and also summarized in the form of an annotated checklist in this paper. All 286 available specimens were morphologically examined. For 138 specimens, the 114 ITS and 85 LSU nrDNA sequences were newly sequenced and used for phylogenetic analysis. In total, we confirm the presence of 153 species of wood-inhabiting poroid and corticioid fungi in Uzbekistan, of which 31 species are reported for the first time in Uzbekistan, including 19 that are also new to Central Asia. These 153 fungal species inhabit 100 host species from 42 genera of 23 families. Polyporales and Hymenochaetales are the most recorded fungal orders and are most widely distributed around the study area. This study provides the first comprehensively updated and annotated the checklist of wood-inhabiting poroid and corticioid fungi in Uzbekistan. Such study should be expanded to other countries to further clarify species diversity of wood-inhabiting fungi around Central Asia.
  • Spirin, Viacheslav; Malysheva, Vera; Haelewaters, Danny; Larsson, Karl-Henrik (2019)
    Stypella vermiformis is a heterobasidiomycete producing minute gelatinous basidiocarps on rotten wood of conifers in the Northern Hemisphere. In the current literature, Stypella papillata, the genus type of Stypella (described from Brazil), is treated as a taxonomic synonym of S. vermiformis. In the present paper, we revise the type material of S. papillata and a number of specimens addressed to S. vermiformis. As a result, the presumed synonymy of S. papillata and S. vermiformis is rejected and the genus Stypella is restricted to the single species S. papillata. Morphological and molecular phylogenetic studies of specimens from the Northern Hemisphere corresponding to the current concept of S. vermiformis uncovered three species from two newly described genera. S. vermiformis s.str. is distributed in temperate Europe and has small-sized basidia and basidiospores, and it is placed in a new genus, Mycostilla. Another genus, Stypellopsis, is created for two other species, the North American Stypellopsis farlowii, comb. nov., and the North European Stypellopsis hyperborea, sp. nov. Basidia and basidiospores of Stypellopsis spp. are larger than in Mycostilla vermiformis but other morphological characters are very similar. In addition, Spiculogloea minuta (Spiculogloeomycetes, Pucciniomycotina) is reported as new to Norway, parasitising basidiocarps of M. vermiformis and Tulasnella spp.